I make flavored yogurt all the time. Though I go for a 'fruit on the bottom' type. I make jam, and when I'm making yogurt I add some of my jam to the bottom of each jar before I pour the milk in. (I make all my yogurt in half pint jars) I have stirred the jam in, but any solids tend to settle so stirring it seems like a waste of time to me. I've also made yogurt with honey, by sweetening the milk with honey as it was heating, before adding the culture.
As for pasteurizing the yogurt after the fact, I personally wouldn't. I like that there's active bacteria in the yogurt. I also think that even though it will continue to get a little more tart (not dramatically though) as it sits in the fridge, the culture helps to delay spoilage.
I also don't know if the consistency would be yogurt like after heating it high/long enough to pasteurize. Yogurt gets thinner when it warms up, would it thicken again when it cooled? I don't know.